I have a
Intel Core i5 3570K @ 3.40GHz
NVIDIA GeForce GTX 680 with a 1920 x 1080 Monitor
and 16 Gigs of RAM, will I be able to run the highest graphical settings? And if yes what are the highest settings to put? (They're all so confusing)

depends on the game, But i'm guessing you'll get 6x scaling on some of the older games (FFX for example) and maybe 4x on some of the GPU intensive games. i haven't tried since buying my 660 ti, but my 560 ti could do at least 3x scaling.

It multiplies the displayed resolution of the game, for example Final Fantasy X is 512x512, with 6x scaling PCSX2 renders it at 3072x3072 then downscales it to whatever resolution you choose to run it at, causing a crisper, sharper image. Similar to Super Sampling for computer games.
Now like i said, Scaling is dependent on the game you're playing. The thing about PCSX2 is that one size doesn't fit all, but it fits most. Zone of Enders is very GPU heavy. So you can't run it at as high of scaling as you could say FFX

Scaling just multiplies the game native resolution and from the GSdx config window,it look like that the maximum you can set for custom resolution is 8192x8192(which is a lot more than 6x native on any game)